Hi,
I've been running into some issues with non-tryptic searches using multiple
enzymes and TPP 4.6.3. It appears that some of the problems are due to
inconsistent enzyme specificity definitions in the different tools.
E.g. for chymotrypsin:
In Tandem2XML the specificity is defined with addEnzyme("chymotrypsin",
"[FLMWY]|{P}");
In ProteolyticEnzymeFactory.cxx the catalog entry is {"chymotrypsin",
"true", NULL, "YWFL|P|false|"}
...but the getProteolyticEnzyme function uses enz->enterSpecificity("YWFM",
"P", False, min_spacing_);
I'm going to make everything consistent on my install here, and wondered if
this would be useful to contribute to the main TPP trunk?
It does depend on picking a single chymotrypsin specificity though - have
no idea which is most appropriate?!
DT
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